Some of them look like they could have been done generatively, Processing, Nodebox or ActionScript or somesuch. I think it's Nodebox that allows you to output your code as PDF's that you can then take into Illustrator with all the layers intact. I've tried to have a go before but it's a bit beyond me

I'd say a combination of things...to me they look like
- some are likely fractal's
- there's definitely some statistical data being plotted onto a graph in there (links project part 2), probably utilises some script on a website to plot a graph
- normal mathematical equations as plotted on a graph
- some look like images taken from a microscope and adjusted in colour/crop etc
- some look like they've been created using a wacom and photoshops tilt/rotate/fade brush tools
- some look like they've used a 'distortion grid' over an original image
- some look like splines have been rotated around the z axis to create the '3d spiral things' and then the whole 3d image is slightly rotated on the x axis to give it a slightly top down look

COMPLEXITY GRAPHICS looks like it uses ies light data (basically it's the luminance and output shape of a light and is usually used in 3d rendering to give accurate lighting) for the shapes as in it's simplest form it's a graph plotting the light if it was seen 'laying flat on a surface' (see attachment)